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Australian-Imaging-Service / pipelines

Scripts to generate analysis pipelines that can be run in XNAT's container service
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[FEATURE] Implement the Whole Slide Imaging (WSI) Datatype and new External Camera Protected (ECP) Datatype in XNAT. #297

Open anzhao opened 2 months ago

anzhao commented 2 months ago

Metadata

Epic: XNAT datatype.

Description

New XNAT data types are needed to store various kinds of research data within the XNAT platform.

Development Stages

  1. Creating a New Data Type Schema in XNAT. Define its structure using an XML schema document (XSD format). This schema specifies the data type’s format and elements. The following is an example:

<?xml version="1.0" encoding="UTF-8" standalone="yes"?>

\AIS research project \ \Mr \An \ZHAO \Sydney Uni \ \{} \ 2. Create an XNAT plugin: The XNAT plugin implemented is a Java archive (JAR) file containing the schema file and additional components for displaying and managing your data type within XNAT. 3. Deploy the XNAT plugin: Once the plugin is built, deploy it on your XNAT server. This process involve copying the JAR file to the plugin folder and restarted your XNAT server to make sure that new data type is loaded into your XNAT system.
github-actions[bot] commented 2 months ago

Stories

anzhao commented 2 months ago

I have turned on the Whole Slide Imaging (WSI) Datatype (xnat:smSessionData) on our XNAT dev server (see image below). Image

I obtained some slide image data from idc open data shared on S3 by installing s5cmd and running the following command: Image

I upload the slide image data to our dev test server and confirmed that XNAT OHIF viewer not support it. Image

By adding QuPath to Neurodesk should be addressed the above issue or alternatively: https://github.com/ImagingDataCommons/slim, this slim code repo seems to address this issue as well.

anzhao commented 2 weeks ago

External Camera Protected Session data (XCPsession) and External Camera Protected Scan data (XCPscan) both limit the access of the datatype by IP address (see below).

Image

RyanPSullivan7 commented 2 weeks ago

In the first instance we won't need it limited by IP as @dean-taylor still needs to look at how we segregate container access, but the creation of the separate data is needed as we will toggle the restrict by IP address at a later date.